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Upgrade dependencies with major impact #204

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97e7879
Upgrade dependencies with major impact (registry-core 4.0.0 development)
Nov 10, 2025
5e0c546
Fix Tomcat instance not starting.
Nov 20, 2025
b0d42da
Fix data access point registration.
Nov 20, 2025
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208 changes: 137 additions & 71 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<groupId>com.github.ukgovld</groupId>
<artifactId>registry-core</artifactId>
<packaging>war</packaging>
<version>2.3.22-SNAPSHOT</version>
<version>3.0.0-SNAPSHOT</version>
<name>Registry Core</name>
<url>http://maven.apache.org</url>

Expand Down Expand Up @@ -86,24 +86,37 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<oltu.oauth2.version>1.0.2</oltu.oauth2.version>
<jersey.version>2.21</jersey.version>
<appbase.version>3.1.4</appbase.version>
<jena.version>3.9.0</jena.version>
<fuseki.version>3.9.0</fuseki.version>
<tomcat.version>7.0.107</tomcat.version>
<lib.version>3.1.3</lib.version>
<shiro.version>1.13.0</shiro.version>
<log4j.version>2.20.0</log4j.version>
<jersey.version>3.1.11</jersey.version>
<appbase.version>4.0.0-SNAPSHOT</appbase.version>
<jena.version>5.5.0</jena.version>
<tomcat.version>11.0.10</tomcat.version>
<lib.version>4.0.0-SNAPSHOT</lib.version>
<shiro.version>2.0.5</shiro.version>
<log4j.version>2.25.0</log4j.version>
<derby.version>10.17.1.0</derby.version>
<jackson.version>2.20.1</jackson.version>
<mockito.version>5.20.0</mockito.version>
</properties>

<dependencies>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-bom</artifactId>
<version>${shiro.version}</version>
<scope>import</scope>
<type>pom</type>
</dependency>
</dependencies>
</dependencyManagement>

<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>provided</scope>
</dependency>
<dependencies>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.12.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
Expand All @@ -122,7 +135,6 @@
<dependency>
<groupId>com.epimorphics</groupId>
<artifactId>appbase</artifactId>
<!-- <version>2.1.1-SNAPSHOT</version> -->
<version>${appbase.version}</version>
<exclusions>
<exclusion>
Expand All @@ -143,32 +155,12 @@
<artifactId>jena-querybuilder</artifactId>
<version>${jena.version}</version>
</dependency>

<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>org.owasp.encoder</groupId>
<artifactId>encoder</artifactId>
<version>1.2.1</version>
</dependency>

<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-core</artifactId>
<version>${tomcat.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-logging-log4j</artifactId>
<version>${tomcat.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-jasper</artifactId>
Expand All @@ -184,23 +176,53 @@
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-multipart</artifactId>
<version>2.21</version>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>4.0.1</version>
</dependency>
<dependency>
<groupId>jakarta.activation</groupId>
<artifactId>jakarta.activation-api</artifactId>
<version>2.1.4</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>2.3.3</version>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-core</artifactId>
<version>${shiro.version}</version>
<classifier>jakarta</classifier>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>${derby.version}</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
<version>${derby.version}</version>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-web</artifactId>
<version>${shiro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>10.14.3.0</version>
<classifier>jakarta</classifier>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-jakarta-ee</artifactId>
<classifier>jakarta</classifier>
</dependency>
<dependency>
<groupId>org.fusesource.stompjms</groupId>
<artifactId>stompjms-client</artifactId>
Expand All @@ -209,12 +231,32 @@
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.12.7.1</version>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.14</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.20.0</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.19.0</version>
</dependency>
<dependency>
<groupId>javax.jms</groupId>
<artifactId>javax.jms-api</artifactId>
<version>2.0.1</version>
<version>2.0.1</version>
</dependency>
<dependency>
<groupId>org.apache.oltu.oauth2</groupId>
Expand All @@ -226,39 +268,47 @@
<artifactId>org.apache.oltu.oauth2.jwt</artifactId>
<version>${oltu.oauth2.version}</version>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20250107</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.5.20</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-fuseki1</artifactId>
<version>${fuseki.version}</version>
<artifactId>jena-fuseki-main</artifactId>
<version>${jena.version}</version>
<exclusions>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<artifactId>jetty-ee10-servlet</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
</exclusion>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
<artifactId>jetty-ee10-servlets</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient-cache</artifactId>
<version>4.5.14</version>
</dependency>
<dependency>
<groupId>com.github.jsonld-java</groupId>
<artifactId>jsonld-java</artifactId>
<version>0.13.2</version>
</dependency>
</dependencies>

<build>
Expand Down Expand Up @@ -290,8 +340,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>21</source>
<target>21</target>
</configuration>
</plugin>

Expand Down Expand Up @@ -359,6 +409,22 @@
<webXml>${basedir}/src/main/webapp/WEB-INF/web.xml</webXml>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.5.3</version>
<configuration>
<properties>
<excludeTags>slow</excludeTags>
</properties>
<argLine>
-javaagent:${settings.localRepository}/org/mockito/mockito-core/${mockito.version}/mockito-core-${mockito.version}.jar
-Xshare:off
-Dtomcat.util.scan.StandardJarScanFilter.jarsToSkip=derby*.jar
--add-opens=java.base/java.net=ALL-UNNAMED
</argLine>
</configuration>
</plugin>
</plugins>

<extensions>
Expand Down
7 changes: 3 additions & 4 deletions src/main/java/com/epimorphics/registry/RegRun.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
package com.epimorphics.registry;

import java.io.File;
import java.net.URL;
import java.net.URI;

import org.apache.catalina.startup.Tomcat;

Expand Down Expand Up @@ -58,11 +58,10 @@ public static void main(String[] args) throws Exception {
}

org.apache.catalina.Context context = tomcat.addWebapp(contextPath, rootF.getAbsolutePath());
context.setConfigFile(new URL("file:src/main/webapp/META-INF/context.xml"));
context.setConfigFile(new URI("file:src/main/webapp/META-INF/context.xml").toURL());

tomcat.getConnector();
tomcat.start();
tomcat.getServer().await();

}

}
4 changes: 2 additions & 2 deletions src/main/java/com/epimorphics/registry/commands/CommandAnnotate.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
import java.net.URI;
import java.net.URISyntaxException;

import javax.ws.rs.core.Response;
import jakarta.ws.rs.core.Response;

import com.epimorphics.registry.core.Command;
import com.epimorphics.registry.core.RegisterItem;
Expand All @@ -33,7 +33,7 @@
import com.epimorphics.registry.webapi.Parameters;
import com.epimorphics.util.EpiException;
import org.apache.jena.rdf.model.ResourceFactory;
import javax.ws.rs.NotFoundException;
import jakarta.ws.rs.NotFoundException;


public class CommandAnnotate extends Command {
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/com/epimorphics/registry/commands/CommandCompare.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@
import org.apache.jena.vocabulary.RDFS;
import org.apache.shiro.SecurityUtils;

import javax.ws.rs.core.Response;
import jakarta.ws.rs.core.Response;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

import static javax.ws.rs.core.Response.Status.*;
import static jakarta.ws.rs.core.Response.Status.*;

public class CommandCompare extends Command {
private static final Double DEFAULT_SIMILARITY = 0.7;
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/com/epimorphics/registry/commands/CommandDelete.java
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Expand Up @@ -21,22 +21,22 @@

package com.epimorphics.registry.commands;

import javax.ws.rs.core.Response;
import jakarta.ws.rs.core.Response;

import com.epimorphics.registry.core.Command;
import com.epimorphics.registry.core.Register;
import com.epimorphics.registry.core.RegisterItem;
import com.epimorphics.registry.core.Status;
import com.epimorphics.registry.message.Message;
import com.epimorphics.registry.store.RegisterEntryInfo;
import javax.ws.rs.NotFoundException;
import jakarta.ws.rs.NotFoundException;
import java.util.ArrayList;
import java.util.List;


public class CommandDelete extends Command {

private List<String> deletedItems = new ArrayList<>();
private final List<String> deletedItems = new ArrayList<>();

@Override
public Response doExecute() {
Expand Down
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